test

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 891b14dc463342e9403aab317fc0877fdd78e82c..80e1ebe1a00e2f56ec19a6f23c3ba890af1c4f10 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -254,7 +254,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                
                TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
         
-               pDataArray->count = pDataArray->lineEnd;
+               pDataArray->count = 0;
                for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
                                   
                        if (pDataArray->m->control_pressed) { 
@@ -281,6 +281,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                        
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
+                pDataArray->count++;
                                
                                int barcodeIndex = 0;
                                int primerIndex = 0;
@@ -398,7 +399,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                     string thisGroup = "";
                     if (pDataArray->createGroup) {
                                                if(pDataArray->barcodes.size() != 0){
-                                                       string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
+                                                       thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
                                                        if (pDataArray->primers.size() != 0) { 
                                                                if (pDataArray->primerNameVector[primerIndex] != "") { 
                                                                        if(thisGroup != "") {